Intercore
by alicecullenrocks888
Summary: Chuck's intersect has more secrets that he has yet to uncover. And it seems like he just had found its biggest one. Read and review!
1. Chapter 1

**A/N: Firstly I'm giving credits to KateMcK for this, SHE BETA'D IT *smiley face*. Secondly, I don't own Chuck. Thirdly, review, and tell me what you think and how i should improve and what you'd like to see in the story. Enjoy! **

An art deco chrome lamp stands in a corner, its multifaceted glass panels gleaming awkwardly in the in the sunlight. Exposed beams, cracked and misshapen, hang from the ceiling like the ribs of a starving cat. A faint whiff of acrid smoke from traffic, intermixed with the smell of the unwashed masses, drift through the window. A late night mix of deadmau5 fills the darkened room with its bright neon glow.

Claudia sighed as she entered her father's room. It was never kept, make that, it was never touched. She understood he was a busy man, but after the loss of a close partner and a spouse, maybe he is on the edge. Claudia had every right to be worried for her father.

Her father was in the stupid computer lab again, and he wouldn't let anyone in. Only ate a meal a day, and Claudia thought it was a waste of hiring a chef.

"All right this is it. I'm dragging him out of there today!" she declared with confidence, but slumped and shuffled out of the room as she continued "and I have never succeeded to this day."

"Dad. Dad. Come out. Dad. There's food here. Come on, you know you want some." Claudia practiced her usual line to lure him out.

"Who do you think I am honey? I'm not falling for that. Your dinner time's not up yet," Claudia mimicked her dad's same old muffled reply as she slowly makes her way to the door.

"Stupid dad never falls for that. Time to change methods," Claudia muttered. "HOLY CRAP, DAD! GET OUT OF THERE NOW! THERE ARE WEIRD EVIL LOOKING CREEPOS RIGHT INSIDE HERE! DAD! THEY'RE COMING FOR ME! HOLY CR- "Claudia didn't even have to finish, because he was already up and out.

"I should have thought of that years ago!"

"Haha, very funny, Claudia. I knew there was no bad guy. Our security system was designed by me and Uncle Stephen. No flaws that I know of. And I was on the way out anyway."

Claudia couldn't believe her ears. Not the flawless part, she already knew that. But going out? She hasn't even done that herself. Literally.

"So where ya goin'? Can I come, oh sweet father of mine?"

"I'm heading to Uncle Stephen's place." He grabbed his coat and swung it over his shoulder. He was surprisingly fit for a man in his forties and never worked out in like, 13 years. He still had that same tousled, dirty blond hair eons ago, but his face had only three expressions that Claudia had ever seen, worried, panicked, and "the boring one".

"Isn't he dead? Or do you mean the cemetery…?" Claudia questioned as she followed her dad into the foyer.

"No, his new place where his family lives. I just need to retrieve some files. Will be back before dinner."

"No, we'll be back before dinner," Claudia deadpanned.

"That's not a good idea Claudia. Don't you know how dangerous this is?" her dad asked, exasperated.

"You like Uncle Stephen right? You trust him right? Then what's so scary about going to his place? Plus, you're going to be there," Claudia retorted. She wasn't going to give up the only chance of getting out of her house. Technically she already was, but she still felt that she needed adventure. And when she gave that reason to her dad about her needing adventure, he said that being in the car now was an adventure already.

Her dad couldn't reply or fight back with Claudia's reason, and all he did was sigh. Plus, they already arrived at Echo Park.

"Oh my gosh, I can't believe it, I'm so excited! Are you?" Claudia gushed as she jumped up and down.

"Honey, don't do that. You're thirteen."

"And being my father, you should know I never act my own age." Claudia rolled her eyes at him, but she wasn't going to let him ruin her mood either.

"Now behave Claudia," He instructed sternly as he knocked on the first door.

The door opened, but not fully. The chain was still on. A woman, with hazel hair and brown eyes, answered.

"Hi, who are you looking for?" she asked.

"Hello, I'm looking for a Chuck Bartowski?"

"And you are?"

"Oh, yes, I'm his godfather. Tell him that. He'll know who I am," he said calmly.

The door slammed shut suddenly and it reopened again before Claudia's father could react.

"Uncle Mark! It's Ellie! Remember?" she gushed. Kinda like Claudia.

"Ellie! Wow, you've grown up. By… a lot." He gestured about her swollen belly.

"Dad, you never told me I had uh, god siblings," Claudia whispered menacingly as she spun him around to face her.

"Yeah… well, this is Ellie, and there is Chuck too." he whispered back. Ellie approached Claudia, and Claudia put on her fakest smile she could handle in this situation.

"Well, Chuck is next door, and he has a kick ass girlfriend so watch out! Oh and by the way, I'm so glad you dropped by to see him. He really likes you, you know. We should go out for a coffee when you're done with Chuck!" Ellie squealed.

"Sure thing Eleanor," Mark smiled as she went back inside.

"Wow, I'm getting old," Mark muttered as he approached the other door.

A stunning blond opened the door this time, without the chain on the door.

"Honey, who is it?" a male voice called out.

"Uhm, I don't know, may I help you?" She replied as her hand snaked behind her back. Mark noticed.

"I'm not a threat." He whispered. Just then, Chuck appeared by Sarah's side.

"Hey! Uncle Mark! This is a nice surprise. What are you doing here?"

"Hi, Chuck, and I assume you must be the 'kick ass girlfriend' Ellie was telling me about," Mark responded.

"Well, Ellie is right as usual. Sarah is pretty much awesome." Chuck steps aside. "Please, come in. I take it you remember Morgan?

Morgan appeared out of the kitchen, waving madly. Chuck was about to close the door when Claudia suddenly called out "HEY, AM I REALLY THAT INVISIBLE?"

"Oh yeah," Mark indicated to the girl behind him, "This is my daughter, Claudia."

"Thank you so much Daddy for remembering and mentioning me," Claudia added sarcastically.

"Claudia…" Mark threatened. "Come on in, and Chuck, I just needed to retrieve a few files your father left. I need it for my research," he continued as he led his daughter into the house.

"Uh, files? You mean the big boxes of file? Those files?"

"Yes, you've seen them? I need one of those boxes labeled 'Aminia'."

"Uncle Mark, I can't give them to you."

"Why not? I made those files too." Mark was getting worried.

"They're… destroyed. Wild, wild fire."

"Chuck, are you still the… you know?" He gestured to Chuck about the Intersect.

"Uh, yeah… why?" Chuck and Sarah grew suspicious.

"Chuck, come here for a moment," Mark said as he led Chuck into his room.

"Now the files are gone you say? Did you download anything else? I believe I actually installed all of 'em into your head too," Mark explained as he searched his bag for his notes. Kind of like his old buddy.

"Now, can you flash on this?" Mark pulled out a picture. A slightly bigger draft than the original Intersect blueprint.

Chuck didn't just flash. He absorbed it all into his head. Yes, from a piece of paper. And as usual, he collapsed and this time blacking out.

Claudia sat on the couch next to Sarah, in unnerving silence. Sarah decided to break that silence.

"So, how is your dad related to Chuck?" Sarah asked, feeling slightly nervous. She just wasn't used to talking to teens.

"Uh, I don't really know, he was friends with Uncle Stephen, they made this super computer thing. And Chuck is uncle Stephen's son. Excuse me, but I think my dad is behaving rather weirdly. Which is normal," Claudia excused herself. She made her way to the room both men were in.

Peeping though the gap between the ajar doors, she saw her father retrieve a piece of paper from his bag. "Flash on this," was all she could hear. Scanning the item her father was holding up once more, Claudia passed out as soon as Bartowski did.

Sarah wondered what was going on. She definitely did not like being the one left out. She made her way up the same path as Claudia and Chuck did, and she did not expect to find an unconscious Chuck and Claudia.

"What is going on here?" she spat out at Mark.

"Look, I think he's just restarting the Intersect. He just downloaded a whole lot of new software and information. Do you mind helping me lift Charles back to bed?" Mark replied nonchalantly, not bothering about Sarah's rising rage. Sarah tightened her lips and gave Mark an icy glare before helping Chuck to bed_._

Then Mark spotted Claudia on the floor.

* * *

Chuck soon regained his consciousness, whereas, Claudia didn't. Mark had been thinking, Claudia passed out too, while snooping around. But it's impossible, he thought. She couldn't have.

But then he remembered. Years back, she was doing her snooping, and managed to get to the Intersect's main processor, the Intercore. She uploaded massive data, more than the Intersect can hold.

"So she really did upload it… the Intercore…" Mark mumbled.

"What are you talking about?" Chuck moaned, his head still pounding.

"How did that happen? That paper, no flash… did you upload something?" Chuck asked.

"Look, hear me out. The paper had information that will link you to the main computer, the one that the Intersect depends on to live, or to even function. It actually transferred the files to your head, all of it. Everything from your father's basement." Mark mumbled, searching his bag again.

"Why my head? Why can't you access them yourself?"

"Because you're on the line. Not even the creator of the main computer, aka, Intercore. If I even tampered with it, your life is on the line. The Intercore and the Intersect isn't meant to be separated. And if so, they have a special connection, but with it in your brain, I have no idea what is going to happen. And I would never have done this, if I had known earlier…"

"Known earlier what? I'm not going to die am I?"

"I'm pretty sure you're not, my son. But I'm not sure for Claudia."

"What do you mean?"

"I mean, Claudia is the Intercore. I didn't know that. But all I know, right now, is that you don't need the governor anymore. You're going to need Claudia."


	2. Chapter 2

**A/N: Yeahhh... this is long overdue, exams are push forward so don't expect a new chapter anytime next week. Hahaha (: again, credits to KateMck for the beta and hope you enjoy this chap (:**

The atmosphere in the house had changed dramatically in the past two hours. One surprise led to another, and it was not the good kind.

"Uncle Mark, would you join us for dinner? I'm sure Ellie would love to have you with us." Chuck was a little too polite, considering Mark was family. But the funny thing was, why hadn't he reappeared earlier? Why wasn't he there with Stephen when Chuck went for his search? What was he doing, as a god father all this while?

There were just too many questions running around in Chuck's mind. And speaking of his MIND, it was lighter, as in like, there was a lesser burden on him, he felt. After that huge knock out, he didn't feel the same as he did five hours ago. He just felt… Good. In a way.

The house was filled with tension and silence, something Chuck would not normally bear. He would usually come up with something and goof around to lighten the mood, but this time, he himself was stuck in it. The only person that felt the most awkward was definitely Sarah. She didn't start off with Mark on a good foot, and adding on to that, she never knew about this, even being in Chuck's life for almost four years. And Chuck was supposed to be the 'open' one.

"Chuck, Sarah, I'm sorry, I didn't expect that this would happen. I shouldn't have come. I promise that if Claudia does not wake up after dinner, I'll be on my way back, with her of course and you will never see me again. Actually even if she did, you still won't." Mark sighed.

"No, no, no, uncle Mark, its FINE! Don't go!' Chuck whined slightly.

"You want me to tell you about your brain right?" Mark sighed once more before continuing. "Come on. And get your girlfriend to scoot over here too."

"Fiancé actually, didn't you receive the invitation?" Sarah smirked as she made her way to both men.

Mark leaned slightly forward, with his hands clasped, and looked Chuck in the eye, although Chuck can't. Motioning to Sarah to not talk about the wedding, he and Ellie knew that they had forgotten about him.

"What do you want to know?"

"The Intersect and Intercore relationship. What's going on in our heads? I don't understand. Plus, I feel a ton better. I still have it right?" Chuck babbled, trying very hard to change the subject

"Easy on the questions, I can only explain one at a time."

Mark continued, " Firstly, the Intersect and the Intercore's relationship is special, like, the Intersect is the software, and the Intercore is the hardware. If something happens to you, she's safe. But if something happens to her, you're gone too."

"You mean if its Claudia goes kaplooey, then Chuck is a smoothie?" Claudia's voice perked up suddenly from the couch. She was propped up on one arm.

"When did you-" Sarah shot her a confused look.

"A few minutes ago actually. Anyway, my head is totally woozy. Did you spike my drink or something? Because MAN, you have to let me know what that was. It totally like blew my mind! Like literally! Flashing images and stuff. Oh hoho, I am so stoked!" Claudia burst out. "Anyway back to the subject, what you're talking about... what is that? I know the Intersect and Intercore, but why are you talking about it?" She continued.

"Wait, how do you know what the Intersect or Intercore is?" Chuck moved closer to her, with this sudden attraction to the young him. A girl version with a hell lot more confidence.

"Uh, I don't really know how to explain... it's like I remember it with like... I really don't know how to put it..." Claudia was literally scratching her head for this.

"Is it like... a series of images? That you understand... like a... a...woah." Like a flash, his eyes were fluttering again.

"Chuck, what is it?" Sarah asked concernedly.

"Did I just read a... Flash?" Chuck was too mind blown for Sarah's question to register.

"I think you did. You know what I mean now? Wow dad, this thing you and Uncle Stephen made... Wow. No wonder you guys barely ate." Claudia half snorted.

"This is amazing! I actually know the blueprints of the Intersect and the Intercore! And mind reading? This telekinesis thing... This is way cool!" Chuck glanced over at Sarah, giving a slight nervous laugh.

Sarah knew of the consequences. Of what is going to happen to Claudia, and Chuck. She knew the blue-prints, and in the end, the CIA is going to rebuild a new intersect, a machine one, and Team Bartowski is over. And Sarah is too attached to the team to let go. Plus, right now, Claudia is now an asset even if the CIA or NSA or whatever isn't going to build a new one. Now she has to protect Claudia too, since she is so closely connected to Chuck. This is going to prove difficult. Way more difficult than it already is.

"That is interesting... Mind reading... Maybe it does have that effect. You can share flashes. You can share thoughts. But only within yourselves." said Mark.

**A/N: If you made it here, PLEASE PLEASE review (: And tell me what 'brain power thingies' you want Claudia and Chuck to share. Oh and it will be a GREAT birthday present if you reviewed. **


End file.
